CTD-2020K17.3

Species: Homo sapiens

Position: chr17: 45238027-45241734

Known as:

Transcript: ENST00000587534

Sequence: Download

Description:

We report a high throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We used the MAGeCK algorithm to identify the top hits by comparing samples from day 30 with day-0 controls. The output of MAGeCK is a set of negatively (or positively) selected lncRNAs, or lncRNAs whose knockout disrupts (or stimulates) cell proliferation. In total, MAGeCK identified 43 negatively selected and 8 positively selected lncRNAs with statistical significance (false discovery rate < 0.25).



sgRNAs

sgRNA_ID Sequence Position (Chr) Position (Lnc) Length PAM Type Validity Cell line Note Ref.
sgRNA1 CAGCCCGGCACTGGCACCGC 45241076-45241095(-) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA2 GCGGTGCCAGTGCCGGGCTG 45241076-45241095(+) gene body (near 5') 20 CGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA3 CAAGGTACCAGTGATGCGGG 45240930-45240949(-) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA4 GGCACTGGCACCGCCGGTGA 45241070-45241089(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA5 CACTGGCACCGCCGGTGAGG 45241068-45241087(-) gene body (near 5') 20 GGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA6 GGTACCAGTGATGCGGGAGG 45240927-45240946(-) gene body (near 5') 20 TGG CRISPRko Partial validated Huh7.5 NA [1]
sgRNA7 CCACAGGGCACACGGGCCAC 45240666-45240685(+) gene body (near 5') 20 AGG CRISPRko Partial validated Huh7.5 NA [1]

GBrowser


Links

lncRNA Function:

sgRNA Design Tool:

Reference

1. Zhu S, Li W, Liu J, Chen CH, Liao Q, et al. (2016). Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nat Biotechnol 34(12): 1279-1286.